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It is necessary to clean wstcref and wstcgrp files which reference 'invalid' TopComponent. Only files stored localy will be deleted. It is responsibility of module developer to define its winsys elements correctly => wstcref and wstcgrp files in module folder (install layer) will not be deleted. One typical example is when some document is opened in editor -> exit IDE -> delete this document -> start IDE -> document cannot be opened -> TopComponent cannot be deserialized typicaly it throws DataObjectNotFoundException. It was handled in ModeData class in previous version of winsys. ModeData is not used now => it must be handled probably in PersistenceManager.getTopComponentForID().
Passing to new winsys owner for evaluation.
Implemented and fixed long time ago, just forgot to close, closing now.